Why Do Some Ngs Read Alignment Software Can Only Be Used To Map Reads Generated By Specific Platforms

Question

[sanchezcavani]

For example, why is SSAHA2 more suitable for 454 but not for Illumina? Why is Novoalign better to be used for Illumina data? Why can some tools be used very widely, like bwa?

Answer 1

[Dan D]

Based on my investigations of the source code way back when, I think it has to do with the fact that a lot of the aligners are written in low-level languages and contain data structures and algorithms highly optimized for certain sizes of data. Sequencers that produce relatively long reads fall outside of the optimal range of some of these aligners. I'm sure someone will give a more elegant answer but that's a quick take.

You'll notice that even tools like bwa have run modes suited for different read lengths.